Question: transcription factor binding site prediction software/server
2
gravatar for bioinformaticssrm2011
4.2 years ago by
India
bioinformaticssrm201180 wrote:

Hi,

I have a DNA sequence (fasta file format), i would like to predict transcription factor binding site ( TFBS) and ribosomal binding sites (RBS). 

Is there an eay software/server which predicts TFBS and RBS. 

I tried to use R package for TFBS prediction using biocLite("JASPAR2014"), but i don't understand it.

Best !

Shashank

ADD COMMENTlink modified 3.4 years ago by oigl60 • written 4.2 years ago by bioinformaticssrm201180
1
gravatar for dago
4.2 years ago by
dago2.5k
Germany
dago2.5k wrote:

It depends which organism are you working with.

Following these links you can find usefull tools:

http://zlab.umassmed.edu/zlab/gene.shtml

http://bip.weizmann.ac.il/toolbox/seq_analysis/promoters.html

 

You can also look Virtual Footprint, " It was especially designed to analyze transcription factor binding sites in whole bacterial genomes and their underlying regulatory networks."

 

 

 

 

ADD COMMENTlink modified 4.2 years ago • written 4.2 years ago by dago2.5k

i am having an prokaryotic sequence.. does above mentioned link work for it

ADD REPLYlink written 4.2 years ago by bioinformaticssrm201180

You should report a bit more in detail what you want to do. I think Virtual Footprint can help you, see my edit.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by dago2.5k
1
gravatar for TriS
4.2 years ago by
TriS3.7k
United States, Buffalo
TriS3.7k wrote:

mapper worked fine for me

ADD COMMENTlink written 4.2 years ago by TriS3.7k

i am having an prokaryotic sequence, so i dont think MAPPER is gonna work....

ADD REPLYlink written 4.2 years ago by bioinformaticssrm201180
1
gravatar for rutial
3.4 years ago by
rutial40
Israel
rutial40 wrote:

You can use Genome Compiler - they have embedded into their software the RBS Calculator by Prof. Howard Salis. 

Here are some helpful articles and tutorial video: How to use, Q&A with Salis, Tutorial video

 

ADD COMMENTlink modified 3.4 years ago • written 3.4 years ago by rutial40
1
gravatar for oigl
3.4 years ago by
oigl60
oigl60 wrote:

You can use weight matrices or SITECON to predict TFBS in UGENE.

ADD COMMENTlink written 3.4 years ago by oigl60
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